2qaa

Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Streptogrisin-B

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 CHLORIDE ION × 4 TYROSINE × 1 LEUCINE × 1 1,2-ETHANEDIOL × 3 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GLYCEROL × 1 ACETIC ACID × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 CHLORIDE ION × 6 TYROSINE × 1 LEUCINE × 1 1,2-ETHANEDIOL × 1 GLYCEROL × 3 ACETIC ACID × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 24	SULFATE ION × 60 CHLORIDE ION × 120 TYROSINE × 24 LEUCINE × 24 1,2-ETHANEDIOL × 48 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 12 GLYCEROL × 48 ACETIC ACID × 36 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRTB_STRGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 115–299 Author chain B； PDBConstruct 1–185； UniProt 115–299

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2qaa
Deposition date deposition_date	2007-06-14
Structure title title	Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3
Keywords keywords	CHYMOTRYPSIN-TYPE SERINE PEPTIDASE, SECOND TETRAHEDRAL INTERMEDIATES, SINGLE AMINO ACIDS, BETA BARRELS, ALPHA HELIX, Hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2qaa__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2qaa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qaa__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.08 Å
Rg (electron density)	14.90 Å
Total Rg	16.03 Å
Atom count	1377
Residues	185
Excluded volume	23950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qaa__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qaa__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2qaa__assembly_3__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Streptogrisin-B
Molecular weight formula_weight	18653.2 kDa
EC 编号 ec_number	3.4.21.81
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3397

ISGGDAIYSSTGRCSLGFNVRSGSTYYFLTAGHCTDGATTWWANSARTTVLGTTSGSSFPNNDYGIVRYTNTTIPKDGTVGGQDITSAANATVGMAVTRRGSTTGTHSGSVTALNATVNYGGGDVVYGMIRTNVCAEPGDSGGPLYSGTRAIGLTSGGSGNCSSGGTTFFQPVTEALSAYGVSVY

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	TYROSINE
Molecular weight formula_weight	181.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	LEUCINE
Molecular weight formula_weight	131.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	521

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qaaa_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.1 — Prokaryotic proteases

Domain ID domain_id	d2qaab_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.1 — Prokaryotic proteases

CATH v4.4 (4 domains)

Domain ID domain_id	2qaaA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2qaaA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2qaaB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2qaaB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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Unit-cell length a length_a	142.286 Å
Unit-cell length b length_b	142.286 Å
Unit-cell length c length_c	142.286 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	1.230 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1133
R_work r_work	0.1125
R_free r_free	0.1271

Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3

1. Protein Identity and Related Structures Protein Identity & Related Structures

Streptogrisin-B

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2qaa__assembly_1__model_1

2qaa__assembly_1__model_1 | I(q)

2qaa__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3

1. Protein Identity and Related Structures Protein Identity & Related Structures

Streptogrisin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2qaa__assembly_1__model_1

2qaa__assembly_1__model_1 | I(q)

2qaa__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)